#!/bin/sh

# run from directory where this script is
cd `echo $0 | sed 's/\(.*\)\/.*/\1/'` # extract pathname
EXAMPLE_DIR=`pwd`

# check whether echo has the -e option
if test "`echo -e`" = "-e" ; then ECHO=echo ; else ECHO="echo -e" ; fi

# function to test the exit status of a job
. ../check_failure.sh

$ECHO
$ECHO "$EXAMPLE_DIR : starting KUBO"
$ECHO

# set the needed environment variables
. ../environment_variables

# required executables and pseudopotentials
BIN_LIST="pw.x dos.x projwfc.x kvecs_FS.x bands_FS.x"


$ECHO
$ECHO "  executables directory: $BIN_DIR"
$ECHO "  pseudo directory:      $PSEUDO_DIR"
$ECHO "  temporary directory:   $TMP_DIR"
$ECHO "  checking that needed directories and files exist...\c"

# check for directories
for DIR in "$BIN_DIR" "$PSEUDO_DIR" ; do
    if test ! -d $DIR ; then
        $ECHO
        $ECHO "ERROR: $DIR not existent or not a directory"
        $ECHO "Aborting"
        exit 1
    fi
done
for DIR in "$TMP_DIR" "$EXAMPLE_DIR/results" ; do
    if test ! -d $DIR ; then
        mkdir $DIR
    fi
done
cd $EXAMPLE_DIR/results

# check for executables
for FILE in $BIN_LIST ; do
    if test ! -x $BIN_DIR/$FILE ; then
        $ECHO
        $ECHO "ERROR: $BIN_DIR/$FILE not existent or not executable"
        $ECHO "Aborting"
        exit 1
    fi
done
 
# check for pseudopotentials
for FILE in $PSEUDO_LIST ; do
    if test ! -r $PSEUDO_DIR/$FILE ; then
        $ECHO
        $ECHO "ERROR: $PSEUDO_DIR/$FILE not existent or not readable"
        $ECHO "Aborting"
        exit 1
    fi
done
$ECHO " done"

# how to run executables
PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX"
KUBO_COMMAND="$PARA_PREFIX $BIN_DIR/kubocalc.x $PARA_POSTFIX"
DOS_COMMAND="$PARA_PREFIX $BIN_DIR/dos.x $PARA_POSTFIX"
PROJWFC_COMMAND="$PARA_PREFIX $BIN_DIR/projwfc.x $PARA_POSTFIX"
KVECS_COMMAND="$BIN_DIR/kvecs_FS.x "
BANDS_COMMAND="$BIN_DIR/bands_FS.x "
$ECHO
$ECHO "  running pw.x as:      $PW_COMMAND"
$ECHO "  running dos.x as:     $DOS_COMMAND"
$ECHO "  running projwfc.x as: $PROJWFC_COMMAND"
$ECHO "  running kvecs_FS.x as:  $KVECS_COMMAND"
$ECHO "  running bands_FS.x as:  $BANDS_COMMAND"
$ECHO
 
# time step for molecular dynamics is in Rydberg atomic units 1 a.u.=4.8378 * 10^-17 s
# phys rev b 38 2 methfessel states fundamental freq of Si is ~42.25 Thz
# 1/10 of fundamental is about 50.0 a.u. then

#the thermal expansion of Mg2Si at 800K is ~42 10^-6 K^-1
# reference anastassakis and hawranek say 6.338 A at 300K
# reference baranek and schamps say 6.351 A at 300K

# by Y. S. Raptis et al. the expansion from 300K to 800K is 2.379%
# so lets take the average of the data and expand by that
# lattice spacing at 800K : 6.4954 (proably more significant digits than valid).

cat > kubo_Mg2Si_24.in << EOF
&control
   calculation = 'scf'
   restart_mode='restart',
   pseudo_dir = '$PSEUDO_DIR',
   outdir='./',
   prefix='Mg2Si24',
   disk_io ='low'
   wf_collect=.true.,
 /
&SYSTEM
    ibrav = 0,
    celldm(1) = 1.889725989,
    ntyp = 2,
    nat = 24,
    ecutwfc =50.0,
    occupations =  'smearing',
    degauss = 0.004,
    smearing = 'fd'
    nosym = .true.
/
 &electrons
    electron_maxstep = 999 ,
    conv_thr = 1.0e-6 ,
    mixing_beta = 0.3 ,
    startingwfc = 'atomic+random' ,
/
&inputpp
    deltarep = 'l',
    check_wfc = .false.,
    temperature = 800.0,
/
ATOMIC_SPECIES
 Si  28.086 Si.pz-vbc.UPF
 Mg  12.0000 Mg.pz-n-vbc.UPF
ATOMIC_POSITIONS (crystal)
 Si      0.00000000  0.00000000  0.00000000
 Mg      0.12500000  0.12500000  0.12500000
 Mg      0.37500000  0.37500000  0.37500000
 Si      0.50000000  0.00000000  0.00000000
 Mg      0.62500000  0.12500000  0.12500000
 Mg      0.87500000  0.37500000  0.37500000
 Si      0.00000000  0.50000000  0.00000000
 Mg      0.12500000  0.62500000  0.12500000
 Mg      0.37500000  0.87500000  0.37500000
 Si      0.50000000  0.50000000  0.00000000
 Mg      0.62500000  0.62500000  0.12500000
 Mg      0.87500000  0.87500000  0.37500000
 Si      0.00000000  0.00000000  0.50000000
 Mg      0.12500000  0.12500000  0.62500000
 Mg      0.37500000  0.37500000  0.87500000
 Si      0.50000000  0.00000000  0.50000000
 Mg      0.62500000  0.12500000  0.62500000
 Mg      0.87500000  0.37500000  0.87500000
 Si      0.00000000  0.50000000  0.50000000
 Mg      0.12500000  0.62500000  0.62500000
 Mg      0.37500000  0.87500000  0.87500000
 Si      0.50000000  0.50000000  0.50000000
 Mg      0.62500000  0.62500000  0.62500000
 Mg      0.87500000  0.87500000  0.87500000
CELL_PARAMETERS (cubic)
 10.60694378  3.75012094  6.49540000
 0.00000000  11.25036282  6.49540000
 0.00000000  0.00000000  12.99080000

K_POINTS (automatic)
 5 5 5 0 0 0

EOF

$ECHO "  running the Kubo calculation for Mg2Si...\c"
env OMP_NUM_THREADS=8 $KUBO_COMMAND <  kubo_Mg2Si_24.in >  kubo_Mg2Si_24.out
check_failure $?
$ECHO " done"

